The incorporation of HIV-1 protease inhibitors (Pis) in 1996 into combination therapy regimens with two or more reverse transcriptase inhibitors has been critical to the reduction of AIDS related mortality, improvement of quality of life, and enhancement of HIV/AIDS management. Highly active antiretroviral therapy (HAART) remains the most effective treatment option for HIV/AIDS, but there are many serious limitations of current treatment regimens. The emergence of multidrug-resistant HIV-1 variants is perhaps, one of the most formidable challenges. In our continuing collaborative research efforts toward developing new generations of protease inhibitors, our structure-based design strategies have led to the design and discovery of protease inhibitor UIC-94017 (later named TMC-114, or darunavir). Darunavir has exhibited marked antiviral activity, excellent drug resistance profiles against multidrug-resistant strains and favorable pharmacokinetic properties. On June 23, 2006, darunavir was approved by the FDA as the first treatment for drug-resistant HIV. Darunavir represents the first of a new generation of inhibitors to combat drug-resistant HIV. However, it is far from ideal for long-term effective treatment. Issues concerning oral bioavailability, pill-burden and possible emergence of resistance over time remain to be answered. Based upon our high resolution X-ray crystal structures of darunavir-bound HIV protease and a number of other protein-ligand structures, we have envisioned a number of intriguing design concepts and developed tools to combat drug-resistance. We have carried out preliminary structure-activity studies and generated a number of small molecule leads. This work now forms the basis of our proposed studies which include: (a) structure-based design and synthesis of bis-THF-derived and nonsulfonamide-based novel drug-like Pis; (b) design and development of novel ligands and scaffolds to improve pharmacological profiles of cylopentyl- tetrahydrofuran (cp-THF)-derived Pis; (c) structure-based design and development of novel templates, scaffolds and heterocyclic ligands to generate novel small molecule drug-like Pis; (d) performance of in- depth drug-resistance studies and determination of X-ray structures of selected inhibitors to gain molecular insight. This research integrates organic synthesis, protein-ligand x-ray crystallography, molecular modeling and in-depth virus and cell-biological studies to design the next generation of HIV-1 protease inhibitors.